rs2829961

Variant names:

• chr21-25869684-T-C
• rs2829961

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.555 in 151,776 control chromosomes in the GnomAD database, including 23,799 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (23799 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.520
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84213 AN: 151658 Hom.: 23768 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.516

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.555 AC: 84302 AN: 151776 Hom.: 23799 Cov.: 30 AF XY: 0.557 AC XY: 41319 AN XY: 74178

African (AFR) AF: 0.647 AC: 26759 AN: 41350

American (AMR) AF: 0.514 AC: 7843 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3468

East Asian (EAS) AF: 0.448 AC: 2299 AN: 5136

South Asian (SAS) AF: 0.585 AC: 2814 AN: 4808

European-Finnish (FIN) AF: 0.553 AC: 5819 AN: 10524

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35352 AN: 67932

Other (OTH) AF: 0.519 AC: 1087 AN: 2096

Alfa AF: 0.531 Hom.: 12749

Bravo AF: 0.557

Asia WGS AF: 0.525 AC: 1827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.78
DANN	Benign	0.53
PhyloP100		-0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2829961; hg19: chr21-27241995;